SLC39A6

solute carrier family 39 member 6, the group of Solute carrier family 39

Basic information

Region (hg38): 18:36108530-36129385

Links

ENSG00000141424 ∙ NCBI:25800 ∙ OMIM:608731 ∙ HGNC:18607 ∙ Uniprot:Q13433 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	0

Variants in SLC39A6

This is a list of pathogenic ClinVar variants found in the SLC39A6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
18-36109613-C-T		not specified	Uncertain significance (Apr 07, 2023)
18-36111086-T-A		not specified	Uncertain significance (Dec 18, 2023)
18-36111178-T-C		not specified	Uncertain significance (May 13, 2024)
18-36111192-T-A		not specified	Uncertain significance (Sep 22, 2023)
18-36111214-C-A		not specified	Uncertain significance (Dec 30, 2023)
18-36111249-C-A		not specified	Uncertain significance (Jan 23, 2023)
18-36112579-C-A		not specified	Uncertain significance (May 29, 2024)
18-36114106-G-T		not specified	Uncertain significance (Jan 09, 2024)
18-36114169-C-T		not specified	Uncertain significance (Oct 27, 2022)
18-36114183-T-A		not specified	Uncertain significance (Jan 04, 2024)
18-36114342-G-A		not specified	Uncertain significance (Oct 05, 2023)
18-36114372-T-C		not specified	Uncertain significance (Jan 24, 2023)
18-36114381-G-A		not specified	Uncertain significance (May 20, 2024)
18-36116676-T-C		not specified	Uncertain significance (Jan 08, 2024)
18-36116710-G-C		not specified	Uncertain significance (Feb 06, 2023)
18-36116763-T-C		not specified	Uncertain significance (Feb 03, 2022)
18-36122152-G-A		not specified	Uncertain significance (Jul 26, 2022)
18-36122167-C-T		not specified	Uncertain significance (Jul 21, 2021)
18-36122170-T-C		not specified	Uncertain significance (Jan 31, 2024)
18-36122222-C-T		not specified	Uncertain significance (Oct 29, 2021)
18-36122228-C-T		not specified	Uncertain significance (Jun 30, 2023)
18-36122231-G-A		not specified	Uncertain significance (Mar 20, 2024)
18-36122244-A-T		not specified	Uncertain significance (Oct 05, 2023)
18-36123502-A-G		not specified	Uncertain significance (Dec 17, 2023)
18-36123539-C-A		not specified	Uncertain significance (Apr 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A6	protein_coding	protein_coding	ENST00000269187	9	20854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.94e-7	0.992	124796	1	39	124836	0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	346	410	0.843	0.0000214	5048
Missense in Polyphen		94	178	0.5281		2151
Synonymous	0.161	147	150	0.983	0.00000815	1420
Loss of Function	2.39	15	28.9	0.519	0.00000167	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000328	0.000328
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000222
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000179	0.000168
Middle Eastern	0.000223	0.000222
South Asian	0.000426	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:12839489}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Zinc influx into cells by the SLC39 gene family;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc transporters (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.701
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.492
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc39a6

Gene ontology

• Biological process: cellular zinc ion homeostasis;zinc ion transmembrane transport;zinc ion import across plasma membrane
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;cell surface;lamellipodium membrane
• Molecular function: zinc ion transmembrane transporter activity